STRUCTURE OF NUCLEIC ACIDS Flashcards
1
Q
Nucleic acids contain only how many monomeric units?
A
4 unique monomeric units
2
Q
Are more difficult to recognize
A
Distinctive sequences
3
Q
2 simple tools make NA sequencing
easier than polypeptide sequencing
A
type II restriction endonucleases
gel electrophoresis
4
Q
Cleave DNA at specific oligonucleotide sites, generating unique fragments of manageable size.
A
Type II
5
Q
separate NA fragments that differ from one another in length by just a single nucleotide
A
Gel electrophoresis
6
Q
Chain termination or dideoxy method was invented by?
A
Frederick sanger
7
Q
It uses enzymatic replication of the DNA to be sequenced
A
Chain termination or dideoxy method
8
Q
Can be carried out on as little as blank of DNA contained in less than 0.1 microliter
A
1 attomole
9
Q
Blank detection of the DNA
A
fluorescent
10
Q
It is more rapid and efficient DNA sequencing technologies
A
Next generation sequencing by Synthesis
11
Q
Next generation is also known as?
A
(UHT) Ultra-High-Throughput sequencing
12
Q
Has developed materials and methods allowing manipulation and analysis of extremely small amounts of biomolecules
A
Nanobiotechnology
13
Q
Blank catalyzes the synthesis of a complementary strand
A
DNA polymerase
14
Q
DNA polymerase catalyzes the synthesis of a complementary strand
A
Sequencing by Synthesis (SBS)
15
Q
Have the advantage in that they can directly detect the addition of each base and record that information in digital form for computer analyses
A
Next-gen Sequencers
16
Q
Hundreds of thousands to hundreds of millions of sequencing reactions can be run at the same time on these instruments
A
Massively Parallel Sequencing
16
Q
Yielding thousands of Blank of sequence information per run
A
Gigabase
16
Q
Also contains information that enables quantification of the amount of each DNA molecule within the library.
A
Digital records
17
Q
The study of the nature and organization of biological information
A
Bioinformatics
18
Q
Bioinformatics includes blank and blank
A
Functional group and proteomics
19
Q
Addresses global issues of gene expression
- Provides new insights into evolutionary relationships between organisms.
A
Functional genomics
20
Q
The study of all the proteins expressed by a certain cell or tissues under specified conditions
A
Proteomics
21
Q
Polynucleotides strands are inherently Blank
A
Flexible
22
Q
Double-stranded DNA is a regular blank with H bonds formed between opposing bases on the 2 chains
A
2 chain structure
23
TRUE OR FALSE
The 2 chains are parallel
False (Anti-parallel)
24
TRUE OR FALSE
The polar sugar-phosphate backbones of the 2 chains are on the inside
False (Outside)
25
Are stacked on the inside of the structure
Bases
26
The DNA has a Blank structure
Ladderlike
27
Base pairs are fixed at Blank apart
0.6 nm
28
This ladderlike structure converts to a blank when given a simple blank
double helix, right-handed twist
29
blank brings the base-pair rungs of the ladder closer together, stacking them blank apart, without affecting the blank distance of 0.6 nm
Helical twisting, 0.34 nm, sugar-sugar
30
This helix repeats itself approximately every blank
10 bp
31
TRUE OR FALSE
Its pitch is 0.34 nm
False (3.4 nm)
32
The major conformation of DNA in solution
B-DNA
33
The base pairing in DNA is size blank
Complementary
34
TRUE OR FALSE
DNA Double helix is an unstable structure
False (Stable)
34
Purines a blank always pair with pyrimidine a blank
Large, Small
35
What makes the DNA Double Helix stable structure?
H bonds
Electrostatic interactions
Van der Waals
Hydrophobic interactions
36
DNA behaves as a blank, flexible molecule
Dynamic
36
TRUE OR FALSE
The Double Helix is not Flexible
False (Flexible)
37
Due to blank DNA is temporarily distort and deform DNA structures over short regions
Localized thermal fluctuations
38
Blank and Blank ensembles of atoms undergo elastic motions on a time scale of nanoseconds (ns)
Base and Backbone
39
These bending influences give the double helix a blank shape
roughly spherical
39
TRUE OR FALSE
The consequences is that the helix bends aggressively
False (gently)
40
Aromatic macrocycles, flat hydrophobic molecules composed of fused, heterocyclic rings.
- Can slip between the stacked base pairs of DNA
Intercalating agents
40
The base pairs move apart to accommodate them, causing a blank of the helix to a more blank structure
unwinding, ladderlike
41
The blank is almost fully extended as successive base pairs are displaced blank from one another
Deoxyribose-phosphate, 0.7 nm
42
The rotational angle about the helix axis between adjacent base pairs is reduced from blank to blank
36 degrees to 10 degrees
42
When duplex DNA molecules are subjected to conditions of pH, temperature, or ionic strength that disrupt base-pairing interactions.
Denatured DNA
43
If temperature is the denaturing agent, the double helix is said to blank
melt
44
Thermal denaturation of DNA can be observed by changes in Blank
UV Absorbance
45
- Absorbance increase
- Aromatic bases in DNA interact via their pie-electron clouds when stacked together in the double helix
Hyperchromic shift
45
DNA denaturation can be followed
spectrophotometrically because the
relative absorbance of the DNA
solution at Blank increases as
much as Blank as the bases unstack
260 nm, 40%
46
UV absorbance of the bases is a consequence of blank
pie-electron transitions
46
The midpoint of the absorbance increase
melting temperature (Tm)
47
TRUE OR FALSE
A:T pairs have higher base stacking energies than G:C pairs
False (G:C is greater)
48
Tm is dependent on the Blank of the solution
ionic strength
49
suppress the electrostatic
repulsion between the negatively
charged phosphate groups in the
complementary strands of the
double helix
Cations
50
is the preferred denaturant
because it does not hydrolyze the
glycosidic bonds linking purine bases
to the sugar-phosphate backbone
Alkali
51
the double-stranded form of DNA is
more stable in?
Dilute salt solutions
52
TRUE OR FALSE
denatured DNA will not renature to reform the duplex structure if the denaturing conditions are removed
False (it will renature)
53
the process occurs more quickly if
the temperature is Blank enough to
promote diffusion of the large DNA
molecules but not so warm as to
cause melting
warm
53
renaturation which requires reassociation of the DNA strands into a double helix
Reannealing
54
TRUE OR FALSE
Renaturation is dependent on both
DNA concentration and time
True
55
TRUE OR FALSE
Many of the realignments are perfect
False (Imperfect)
56
The blank of DNA is an excellent indicator of the sequence complexity of DNA.
Renaturation rate
56
The DNA of bacteriophage T4 contains how many base pairs?
2 x 105 base pairs
57
E. coli chromosomes contain how many base pairs?
4.64 x 106 base pairs
58
E.coli is considerably more blank in that it encodes more information
complex
59
TRUE OR FALSE
It will take shorter for the E.coli DNA strands to find their complementary partners and reanneal
False (longer)
60
The rate of DNA duplex formation depends on complementary DNA sequences encountering one another and beginning the process of sequence blank and blank
alignment and reannealing
61
different DNA strands of
similar sequence can form?
Hybrid Duplexes
62
* DNA from 2 different species are
mixed, denatured, and allowed to
cool slowly so that reannealing can
occur
* DNA from one species is similar in
nucleotide sequence to the DNA of
the other
Hybrid duplexes
62
degree of hybridization is a measure
of the sequence Blank or
blank between the 2 species
similarity or relatedness
63
DNA hybrids can be
created Blank if ss-DNA is allowed
to Blank with RNA copies of itself
in vitro, anneal
64
about Blank of the DNA from a human form
hybrids with mouse DNA
25%
65
* reveal evolutionary relationships
* gives researchers the power to
identify specific genes selectively
against a vast background of
irrelevant genetic material
NA hybridization
66
* an appropriately labeled
oligonucleotide or polynucleotide
* its sequence is complementary to a
target gene
* specifically base pairs with the target
gene, allowing ID and subsequent
isolation of the gene
* assay quantitative expression of genes
(amount of mRNA synthesized)
Probe
67
* naturally occurring
* self-replicating
* extrachromosomal DNA molecules
* found in bacteria
* carry genes specifying novel
metabolic capacities advantageous
to the host bacterium
Plasmids
68
* in duplex DNA, the two
strands are wound about
each other once every
10 bp, i.e., once every
turn of the helix
* ds circular DNA or linear
DNA duplexes whose
ends are not free to
rotate
Supercoils
69
more than the normal number of
turns
Overwound DNA
70
fewer than the normal number of
turns
Underwound DNA
71
How many diameter does the human cell has?
20 um
72
How many pairs of ds-DNA molecules in the
form of chromosomes the human cell has?
23 pairs
73
average length of human cell
= 3 x 109 bp/23 or 1.3
108 nucleotide pairs
74
Blank molecules more than 2 m
of DNA that must be packaged into a
nucleus 10 um in diameter
46 dsDNA
75
the DNA must be condensed by a
factor of more than
105
76
1st stage of this condensation is
accomplished by neatly wrapping the
DNA around protein spools called
nucleosomes
77
are the Fundamental
Structural Unit in Chromatin
Nucleosomes
78
the DNA in a eukaryotic cell nucleus
during the interphase between cell
divisions exists as a nucleoprotein
complex → Blank
chromatin
79
* abundant
* play an important role in chromatin
structure
Histones
79
2 classes of chromatin proteins
* histones
* nonhistone chromosomal proteins
80
* a great variety of different proteins
* involved in genetic regulation;
* only a few molecules of each per cell
nonhistones
81
5 distinct histones
H1, H2A, H2B, H3, H4
82
(+)ly charged, Blank and blank that interact via ionic bonds
with the (-)ly charged phosphate
groups on the polynucleotide
backbone
arg- or lys-rich proteins
83
a 3-domain protein, organizes an
additional 29–43 bp of DNA and links
consecutive nucleosomes
Histone H1
84
each complete nucleosome unit
contains Blank of DNA
176–190 bp
85
the N-terminal tails of histones blank and blank are accessible on the surface
of the nucleosome
H3 and H4
86
residues in these tails can
be covalently modified
* lys and ser
87
may be
acetylated, methylated, or
ubiquitinated
lys
88
may be phosphorylated
ser
89
play an important role
in chromatin dynamics and gene
expression
modifications
90
* a single nucleosome and its associated
H1 linker
chromatosome
91
the DNA double helix has a diameter
of about?
2 nm
92
the total length of the 46 DNA
molecules in a human cell is roughly
2 meters
93
all this DNA must be contained
within the Blank, around 10 mm in
diameter
nucleus
94
the first stage in DNA compaction is blank
wrapping it around nucleosomes
95
in cells undergoing blank, the
chromatin of each chromosome has
been duplicated and highly
condensed in preparation for
distribution to the 2 daughter cells.
mitosis
95
chromosomes are structurally
dynamic
96
in the nuclei of Blank (cells
that are not undergoing mitosis), the
chromatin of each chromosome is
dispersed, and despite its flexibility
and limited compaction, it is not
entangled with the chromatin of
other chromosomes
interphase cells
97
rich in ds regions that form when
complementary sequences within
the chain come together and join via
Blank base pairing
intrastrand
97
* single-stranded
* has a much greater number of
conformational possibilities than
DNA
RNA molecules
98
* base-paired regions
loop
* unpaired regions between base pairs
Stem
99
paired regions of RNA cannot form
B-DNA-type double helices because
the Blank are a steric hindrance to this conformation
RNA 2’-OH groups
100
* most prominent 2 structural
elements in RNA
* both tRNA and rRNA have large
amounts of A-form double helix
A-form double helices
101
Defined structural motifs recur within
the loops of stem-loop structures
1. U-turns
2. Tetraloops
3. Bulges
4. Junctions
102
* a loop motif of consensus sequence
UNRN, N = any nucleotide; R = purine
U-turn
103
* 4-nucleotide loops found at the
termini of stem-loop structures
Tetraloops
104
* internal loops
* the RNA strand is forced into a short
ss loop because one or more bases
along one strand in an RNA double
helix finds no base-pairing partners
Bulges
105
* regions where several stemloop
structures meet
Junctions
106
4 basic 2 structural elements in RNA
* stems
* loops
* bulges
* junctions
107
Other 3 structural motifs
* coaxial stacking
* pseudoknot formation
* ribose zippers
108
* the blunt, nonloop ends of
stemloops situated next to one
another in the RNA sequence stack
upon each other to create an
uninterrupted stack of base pairs
coaxial stacking
108
acceptor end of the L-shaped tRNA is formed by
coaxial stacking of the Blank
acceptor stem on the TC
stem-loop
109
anticodon end is formed by
coaxial stacking of the
Blank on the anticodon stem-loop
dihydrouracil stem-loop
110
* occur when bases in the
loops of stem-loop
structures form a short
double helix by base
pairing with nearby ss
regions in the RNA
Pseudoknots
111
* found when 2 antiparallel, ss regions
of RNA align as an H-bonded
network forms between the 2’-OH
groups of the respective strands, the
O at the 2’-OH position of one strand
serving as the H-bond acceptor while
the H on the 2’-OH of the other
strand is the H-bond donor
ribose zippers
112
* contain 73 to 94 nucleotides in a single
chain
* majority of the bases are H bonded to
one another
tRNA molecules
113
hairpin turns bring Blank of bases in the chain into contact so that double helical regions
form, creating stem-loop 2 structures
complementary stretches
114
each cloverleaf consists of Blank—3 loops and the stem where the 3- and 5-ends of the
molecule meet
4 basepaired segments
115
4 segments
* acceptor stem
* D loop
* anticodon loop
* TC loop
116
the carboxyl group of an AA is linked
to the 3’-OH of the 3’-terminal A
nucleotide, thus forming an Blank
aminoacyl ester
116
* where the AA is linked to form the
aminoacyl-tRNA derivative
acceptor stem
117
often contains dihydrouridine, or D,
residues
D loop
118
unusual bases:
inosine, thiouridine,
pseudouridine, hypermethylated
purines
119
* a double helical segment and 7
unpaired bases, 3 of which are the
anticodon
anticodon stem-loop
120
* a 3-nucleotide unit that recognizes
and base pairs with a particular
mRNA codon
anticodon
121
* a complementary 3-base unit in
mRNA providing the genetic info that
specifies an AA
codon
122
* varies from tRNA to tRNA in the
number of residues that it has
extra or variable loop
123
* most of the invariant residues
common to tRNAs lie within the nonH-bonded regions of the cloverleaf
structure
TC stem-loop
124
* arises from base-pairing
interactions between
bases in the D loop with
bases in the variable
and TC loops
tRNA 3 Structure
124
* 7 unpaired bases, including the
sequence T C ( = Blank)
pseudouridine
125
these interactions fold the D and
TC arms together and bend the
cloverleaf into the stable Blank
L-shaped 3 form
126
the defining feature of an mRNA is
its Blank
primary structure
127
* nucleotide sequence is translated by
Blank into a unique AA
sequence
ribosomes
128
mRNA folds back on itself, forming
Blank, as well as more Blank
stem-loop 2 structures, complex 3 structures
128
Blank provides the structural
framework of the ribosome
rRNA
129
the Blank, whose sequences are not
constrained by the necessity of
encoding a protein, often show
higher orders of structure
5′- and 3’-untranslated regions
130
Blank for the small ribosomal
subunit
16S rRNA
131
* Blank is for the large
ribosomal subunit
23S and 5S rRNAs
132
the Blank is a ribozyme
23S rRNA
133
* a large degree of intrastrand sequence
complementarity is found in all
ribosomal RNA strands
rRNA 2 Structure
134
the loop regions of stem-loops contain
U-turns, tetraloops, and bulges
135
* when ribosomal proteins combine
with rRNAs and when the ensuing
ribonucleoprotein complexes, the
small and large subunits, come
together to form the complete
ribosome
rRNA 3 Structure
